Being the silly person I am, I accidentally used clean command in DISKPART on the wrong HDD (external via USB). I know all the data is still there as I didn't use the all parameter, and I even remember where the partition starts, one is NTFS or FAT32 and the other is ext3.
Right now the HDD is just a blob of unrecognized space, is there anyway to rebuild the indexes on the partitions? All the important data is on the NTFS/FAT32 HDD. Oh, and preferably a way to pause and resume is crucial too.